Blastall run from CGI script

andrew_walsh at my-deja.com andrew_walsh at my-deja.com
Thu Sep 14 15:31:52 EST 2000


Hi everyone,

I'm a newbie to the usenet community so please excuse my format,
syntax...

I've been trying to run blastall from a CGI script on a Linux (RH 6.2)
machine.  The blastall program and Apache web server are on the same
machine.  I can run the program via perl scripts from the command line
without problem.  But when I create the cgi script and execute it from
the web page I get the same error message in my httpd error_log file-
[blastall] WARNING: could not find index files...

I've already used formatdb to create these index files.  The correct
path is given in the CGI script.  My webserver (user, group: http) owns
all of these files.  All of these files are in the home directory of
http (not httpd).

The .ncbirc file has been created with appropriate paths for Data and
BLASTDB.  This file has been put in what I can imagine would be every
possibly relevant directory (dir containing blastall, cgi-bin dir, http
home dir).

I'm using the Open2 module to open a file handle for the blastall
program and sending sequence from a file as input.  Then I have the
results sent as standard output back to the web page.

I just get the header for the Blast result and then query length (this
isn't even right since it says 15 letters, not the actual length of the
sequence in the file referened in the cgi script).  I could well be
wrong, but I don't think that the problem is my relative newbie status
in cgi- I can get echo to send STDOUT to the web page.

If anyone has any ideas on what I'm doing wrong or overlooking they
would be greatly appreciated.
THANKS!!

Andrew


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